The LDSB investigates the organization and activities of developmental regulatory networks using formation of the Drosophila embryonic heart and body wall muscles as a model system. The overarching goal of this work is to comprehensively identify and characterize the upstream regulators of cell fate specification, the downstream effectors of differentiation, and the complex functional interactions that occur among these components during organogenesis. To achieve this objective, we combine contemporary genome-wide experimental and computational approaches with classical genetics and embryology to generate mechanistic hypotheses that we then test at single cell resolution in the intact organism. Genome-wide gene expression profiling carried out in an independent project, combined with a survey of the literature, uncovered numerous transcription factors (TFs) that are expressed in various subsets of mesodermal cells at different developmental stages. For many of these TFs, prior genetic studies have implicated an important role in muscle and/or heart development. However, in most cases, the DNA binding specificities and regulatory targets of these TFs have not been characterized. To address this critical knowledge gap, we have initiated a systematic analysis of the sequences bound by mesodermal TFs using the protein binding microarray (PBM) technology developed by our collaborators in Dr. Martha Bulyks laboratory at Brigham and Womens Hospital and Harvard Medical School. To date, we have completed PBM analysis of 40 Drosophila mesodermal TFs. Our most comprehensive PBM dataset for a single family of TFs corresponds to a group of Drosophila homeodomain (HD) proteins that are localized to the mesoderm where they function to specify numerous cell type identities. By using universal PBMs to interrogate all possible binding site sequences, we identified distinct sets of 9-mers that are bound by different HD proteins, in addition to sequences that are bound by all HDs, consistent with other recent findings. The identification of HD-preferred binding sites has been critical to our subsequent studies of myoblast-specific gene regulatory networks. In the case of other TF families, we have used available PBM and related data from other species to infer the DNA binding specificities of orthologous Drosophila TFs in order to design functional studies of gene regulatory models. Collectively, these investigations serve as a paradigm for how in-depth knowledge of TF binding sites can be utilized to dissect the molecular mechanisms responsible for generating the unique genetic programs of individual cells during development.